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David Zhang
Experienced bioinformatician who enjoys learning and applying the best practices for method development. I focus on developing robust, user-friendly tools that harness transcriptomic data to improve the rate of genetic diagnosis.
Education
PhD, Bioinformatics
University College London
London, UK
Present - 2017
- Thesis: Using transcriptomics to improve the genetic diagnosis rate of rare disease patients.
MSc, Neuroscience
University College London
London, UK
2016 - 2015
- Thesis: The role of mitochondrial dysfunction in Xerodoma pigmentosum
- Grade: Merit (68%)
- Awarded post-graduate support scheme bursary (£10,000)
BSc, Biomedical science
University College London
London, UK
2015 - 2012
- Thesis: Investigating the function of CYFIP1 in the development of rat hippocampal neurons.
- Grade: 2:1 (69%)
H.S.
Queen Elizabeth’s School
Barnet, UK
2012 - 2007
- Grades: Maths (A*), Biology (A*), Chemistry (A*), Sociology (A).
Work Experience
Bioinformatician internship (2 months)
Remote, US
2021
- Goal: Set up an aberrant splicing detection pipeline for drug target discovery in C9orf72 ALS patients.
- Used docker to setup a reproducible workflow for running aberrant splicing analyses on an AWS instance.
Research Technician
University College London
London, UK
2017 - 2016
- Goal: Investigate the impact of genetic variation on the age of onset of dementia and cognition within Down syndrome patients.
Software & programming
Bioconductor packages
N/A
N/A
Present - 2020
- dasper: Detection of aberrant splicing events in RNA-sequencing. Author and maintainer.
- megadepth: BigWig and BAM related utilities. An R wrapper for the megadepth software developed by Chris Wilks. Co-author and maintainer.
- ODER: Optimising the definition of Expressed Regions. Submitted to Bioconductor. Co-author and maintainer.
R packages
N/A
N/A
Present - 2022
- ggtranscript: Visualising transcript structure and annotation using ggplot2. Author and maintainer.
- autorecipes: Automate your recipe planning. Author and maintainer.
Python packages
N/A
N/A
Present - 2021
- autogroceries: Automate your grocery shop. Author and maintainer.
- codino converts a codon design to the expected amino acid frequencies, and vice versa. Author and maintainer.
Web scraping
N/A
N/A
2021
- Applied the python packages Beautiful Soup and Selenium to web scrape information on all UK biotechnology companies.
Teaching Experience
Developing Bioconductor packages
University College London
Virtual Event
2020
R package development
Rstats club
Virtual Event
2020
- Presentation about unit testing fundamentals, the importance of testing and new features released in the R package testthat edition 3.
- Presentation about pre-commit hooks in R.
- Presentation about the best practices of developing R packages.
R fundamentals
Clinician Coders
London, UK
2020 - 2018
- Developed materials and lead workshops that aimed to teach R fundamentals to clinicians.
RNA-sequencing for diagnostics
Kings College London
London, UK
2020 - 2017
- Lectured graduate level students about how transcriptomics can be applied in the diagnostic pipeline.
Selected Publications
recount3: summaries and queries for large-scale RNA-seq expression and splicing
Genome Biology
N/A
2021
- Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B
- Role: Adviser.
- DOI: https://doi.org/10.1186/s13059-021-02533-6
Developmental Consequences of Defective ATG7-Mediated Autophagy in Humans
The New England Journal of Medicine
N/A
2021
- Collier J, Guissart C, Oláhová M, Sasorith S, Piron-Prunier F, Suom Fi, Zhang D, Martinez-Lopez N, Leboucq N, Bahr A, Azzarello-Burri S, Reich S, Schöls L, Polvikoski TM, Meyer P, Larrieu L, Schaefer AM, Alsaif HS, Alyamani S, Zuchner S, Barbosa IA, Deshpande C, Pyle A, Rauch A, Synofzik M, Alkuraya FS, Rivier F, Ryten M, McFarland R, Delahodde A, McWilliams TG, Koenig M, and Taylor RW.
- Role: Analyst
- DOI: https://doi.org/10.1056/NEJMoa1915722
Megadepth: efficient coverage quantification for BigWigs and BAMs
Bioinformatics
N/A
2021
- Wilks C, Ahmed O, Baker DN, Zhang D, Collado-Torres L, Langmead B.
- Role: R package developer.
- DOI: https://doi.org/10.1093/bioinformatics/btab152
Integration of eQTL and Parkinson’s disease GWAS data implicates 11 disease genes
Jama Neurology
N/A
2021
- Kia DA, Zhang D, Guelfi S, Manzoni C, Hubbard L, United Kingdom Brain Expression Consortium (UKBEC), International Parkinson’s Disease Genomics Consortium (IPDGC), Reynolds RH, Botía JA, Ryten M, Ferrari R, Lewis PA, Williams N, Trabzuni D, Hardy J, Wood NW.
- Role: Co-first author.
- DOI: https://doi.org/10.1001/jamaneurol.2020.5257
Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders.
Science advances
N/A
2020
- Zhang D, Guelfi S, Ruiz SG, Costa B, Reynolds RH, D’Sa K, Liu W, Courtin T, Peterson A, Jaffe AE, Hardy J, Botia JA, Collado-Torres L and Ryten M.
- Role: First Author.
- DOI: https://doi.org/10.1126/sciadv.aay8299
Regulatory sites for known and novel splicing in human basal ganglia are enriched for disease-relevant information.
Nature Communications
N/A
2020
- Guelfi S, D’Sa K, Botía J, Vandrovcova J, Reynolds RH, Zhang D, Trabzuni D, Collado-Torres L, Thomason A, Leyton PQ, Gagliano SA, Nalls MA, UK Brain Expression Consortium, Small KS, Smith C, Ramasamy A, Hardy J, Weale ME & Ryten M.
- Role: Analyst.
- DOI: https://doi.org/10.1038/s41467-020-14483-x
Genetic variability in response to Aβ deposition influences Alzheimer’s risk.
Brain Communications
N/A
2019
- Salih DA, Bayram S, Guelfi S, Reynolds RH, Shoai M, Ryten M, Brenton JW, Zhang D, Matarin M, Botia JA, Shah R, Brookes KJ, Guetta-Baranes T, Morgan K, Bellou E, Cummings DM, Escott-Price V, Hardy J.
- Role: Analyst.
- DOI: https://doi.org/10.1093/braincomms/fcz022
Duplication of 10q24 locus: broadening the clinical and radiological spectrum.
Eur J Hum Genet
N/A
2019
- Holder-Espinasse M, Jamsheer A, Escande F, Andrieux J, Petit F, Sowinska-Seidler A, Socha M, Jakubiuk-Tomaszuk A, Gerard M, Mathieu-Dramard M, Cormier-Daire V, Verloes A, Toutain A, Plessis G, Jonveaux P, Baumann C, David A, Farra C, Colin E, Jacquemont S, Rossi A, Mansour S, Ghali N, Moncla A, Lahiri N, Hurst J, Pollina E, Patch C, Ahn JW, Valat AS, Mezel A, Bourgeot P, Zhang D, Manouvrier-Hanu S.
- Role: Analyst.
- DOI: https://doi.org/10.1038/s41431-018-0326-9
Variation at the TRIM11 locus modifies Progressive Supranuclear Palsy phenotype.
Annals of Neurology
N/A
2018
- Jabbari E, John W, Tan MMX, Maryam S, Pittman A, Ferrari R, Mok KY, Zhang D, Reynolds RH, de Silva R, Grimm MJ, Respondek G, Muller U, Al-Sarraj S, Gentleman SM, Lees AJ, Warner TT, Hardy J, Revesz T, Hoglinger GU, Holton JL, Ryten M and Morris HR.
- Role: Analyst.
- DOI: https://doi.org/10.1002/ana.25308
Conferences
The British Society for Genetic Medicine (BSGM)
N/A
Virtual Event
2021
- Talk: dasper: detecting aberrant splicing events in RNA-sequencing data
EuroBioc
N/A
Virtual Event
2020
- Talk: dasper: detecting aberrant splicing events in RNA-sequencing data
Genomics England Research Conference
N/A
London, UK
2019
- Poster: Predicting disease-causing genes using machine learning
Genomics of Rare Disease
N/A
Cambridge, UK
2019
- Poster: The use of transcriptomics to improve gene annotation
- Poster: Using machine learning to understand and predict genes causing rare neurological disorders
- Awarded prize for the best poster (£100)
International Parkinson’s Disease Genomics Consortium (IPDGC)
N/A
Lisbon, Portugal
2019
- Talk: Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders
European Society of human genetics (ESHG)
N/A
Milan, italy
2018
- Poster: Incomplete annotation of OMIM genes is likley to be limiting the diagnostics yield from genetic tests.
International Parkinson’s Disease Genomics Consortium (IPDGC)
N/A
Reykjavik, Iceland
2018
- Poster: Incomplete annotation of OMIM genes is limiting the diagnostic yield from genetic tests.
World Science Conference Israel (WSCI)
N/A
Jerusalem, Israel
2015
- 1 of 11 UK participants chosen to attend.